class: center, middle, inverse, title-slide .title[ # Open Science <br>in MARVLS ] .author[ ### Eva Schemmel <br>NOAA Fisheries ] .date[ ### 2023-04-14 ] --- layout: true .footnote[U.S. Department of Commerce | National Oceanic and Atmospheric Administration | National Marine Fisheries Service] --- ## Am I qualified to give this presentation? I would wager that this feeling is shared among most of us. The myths I tell myself: * I am not a good enough coder * I don't know github well enough * There are errors in my analysis that will be discovered * There are many NOAA policies and forms prevent me from joining in --- ## Open Science State of Mind * (Openscapes Mindset) [https://docs.google.com/presentation/d/1giEW0EIYVnxneGpOBSJnEqg-1CVBUGrbH8Z5gawdeBc/edit#slide=id.p] --- ## Tools & Tricks That Make it Possible --- ## Resources Available * [Openscapes](https://www.openscapes.org/) -[Cohorts - science centers and group shared learning](https://drive.google.com/drive/folders/10MykRskNoP4E0YCwup8rzIeZVm2gA3fO) -Julia Lowndes (julia@openscapes.org) * [NMFS R user group](https://nmfs-opensci.github.io/NMFS-R-UG/) -For information on upcoming meetings and resources -Eli Homes and many more * [NMFS Openscience Repo](https://github.com/orgs/nmfs-opensci/repositories) -Github guide -Quarto simple website template -Quarto report -Xaringan presentation (template used for this presentation) * [NOAA Fisheries Toolbox](https://noaa-fisheries-integrated-toolbox.github.io/) -Kathryn Doering --- ## Examples - Repeatable Reports .left-column[ * [R Markdown Biosampling Inventory Report](https://repository.library.noaa.gov/view/noaa/45018) -Three Regions -Hundreds of Species -Updated Annually - [Github Repo](https://github.com/NOAA-LHP/Biosampling-Inventory) ] .right-column[ <img src="data:image/png;base64,#temp.png" width="400" height="400" /> ] --- ## Getting Started with Quarto and NOAA templates --- ## Examples -Supplimentary Files for Publications * [Schemmel & Dahl 2023](https://github.com/MARVLS/Fish-Gonad-Staging/tree/main/analyses/Variola_louti_Schemmel_2023)  * McBride example --- ## Examples MARVLS Website * (Simple website template)[] * New quarto template available --- ## MARVLS Website Purpose Support MARVLS to: * Hold meetings and workshops * standardize methodology * share accomplishments and challenges * provide mentorship * increase collaboration among scientists --- ## MARVLS Websites & Github Organization * [MARVLS Website]() Organize quarterly workshops and share MARVLS content * [MARVLS Learning Center]() Share code and analysis, recent MARVLS papers,fish developmental sequences, histology interpretation, stains, etc * NOAA policy approved - policies enforced differently at each science center  --- ## How to Contribute 1 .left-column[ [Please use issues for requesting changes to content](https://github.com/MARVLS/MARVLS/issues) * Request change to text or report a typo * Request format change ] .right-column[ .hand-blue[  ] ] --- ## How to Contribute 2 .left-column[ [Add Analyses ](https://github.com/MARVLS/Fish-Gonad-Staging/tree/main/analyses) * Add R code for reproduction assessments here * Use Pull Requests ] .right-column[ .hand-blue[  ] ] --- ## How to Contribute 3 [Add New Content ](https://docs.google.com/spreadsheets/d/1uC-vGAvOSiUSke6Y5pjCHCtO8hYK2HbuVZVa9b2t2p8/edit?usp=share_link) * [Shared Drive -Contribute](https://drive.google.com/drive/u/0/folders/1YeBkEyTUlrrj5RuktUUJJ42J0cS9t_Vp) * Suggest new content * Use google sheet * Add the files that are not available online into the "Contributions" folder  --- ## Histology Reference Template .left-column[ [A template to document developmental sequences.](https://docs.google.com/presentation/d/1l6yKgd4srDlrYsEKtlQsRh-1FmZTicOrgmigT4Az-lo/edit#slide=id.p3) * This template is useful for teaching and provides additional details that make them great references. ] .right-column[ .hand-blue[  ] ]